Search for Variation information by Variation ID:
Detailed information for vg0714225909:
| Variant ID: vg0714225909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14225909 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGACTACGGGAGCGCCACAACTACATCTTCCACGACACGGCGTACCGGTTCCACCCTCGTCGAGCCAGCGGCAGTGATGTCAGTTCCTTCCGTCCGACA[G/A]
CCGGCGAGAACGACACCACCTTTGGTCACATGTGCGCTGTGATGAGGGGGATGGACAGGATGCACTCGGACCTGCACAAGGCGTCCAAGGCCTTGAATGA
Reverse complement sequence
TCATTCAAGGCCTTGGACGCCTTGTGCAGGTCCGAGTGCATCCTGTCCATCCCCCTCATCACAGCGCACATGTGACCAAAGGTGGTGTCGTTCTCGCCGG[C/T]
TGTCGGACGGAAGGAACTGACATCACTGCCGCTGGCTCGACGAGGGTGGAACCGGTACGCCGTGTCGTGGAAGATGTAGTTGTGGCGCTCCCGTAGTCTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.00% | 3.60% | 3.13% | 20.29% | NA |
| All Indica | 2759 | 81.70% | 3.10% | 3.59% | 11.63% | NA |
| All Japonica | 1512 | 57.00% | 0.10% | 1.85% | 41.07% | NA |
| Aus | 269 | 62.10% | 29.70% | 7.06% | 1.12% | NA |
| Indica I | 595 | 72.30% | 4.20% | 5.04% | 18.49% | NA |
| Indica II | 465 | 91.60% | 0.20% | 2.58% | 5.59% | NA |
| Indica III | 913 | 82.90% | 3.20% | 2.52% | 11.39% | NA |
| Indica Intermediate | 786 | 81.40% | 3.90% | 4.33% | 10.31% | NA |
| Temperate Japonica | 767 | 68.20% | 0.00% | 0.78% | 31.03% | NA |
| Tropical Japonica | 504 | 36.90% | 0.00% | 3.37% | 59.72% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.40% | 2.07% | 34.02% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 2.22% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714225909 | G -> DEL | LOC_Os07g24980.1 | N | frameshift_variant | Average:14.12; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
| vg0714225909 | G -> A | LOC_Os07g24980.1 | missense_variant ; p.Ala120Thr; MODERATE | nonsynonymous_codon ; A120T | Average:14.12; most accessible tissue: Minghui63 young leaf, score: 24.836 | benign  |
0.716 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714225909 | 5.75E-06 | 5.76E-06 | mr1340 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0714225909 | 2.98E-06 | 2.98E-06 | mr1381 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |